mirror of
https://git.gfz-potsdam.de/naaice/poet.git
synced 2025-12-15 12:28:22 +01:00
Stop tracking bin/ folder
This commit is contained in:
rastogi
parent
72775432fe
commit
7d459769fd
@ -1,123 +0,0 @@
|
||||
## Time-stamp: "Last modified 2024-12-11 16:08:11 delucia"
|
||||
|
||||
cols <- 1000
|
||||
rows <- 1000
|
||||
|
||||
dim_cols <- 50
|
||||
dim_rows <- 50
|
||||
|
||||
ncirc <- 20 ## number of crystals
|
||||
rmax <- cols / 10 ## max radius (in nodes)
|
||||
|
||||
set.seed(22933)
|
||||
|
||||
centers <- cbind(sample(seq_len(cols), ncirc), sample(seq_len(rows), ncirc))
|
||||
radii <- sample(seq_len(rmax), ncirc, replace = TRUE)
|
||||
mi <- matrix(rep(seq_len(cols), rows), byrow = TRUE, nrow = rows)
|
||||
mj <- matrix(rep(seq_len(cols), each = rows), byrow = TRUE, nrow = rows)
|
||||
|
||||
tmpl <- lapply(seq_len(ncirc), function(x) which((mi - centers[x, 1])^2 + (mj - centers[x, 2])^2 < radii[x]^2, arr.ind = TRUE))
|
||||
|
||||
inds <- do.call(rbind, tmpl)
|
||||
grid <- matrix(1, nrow = rows, ncol = cols)
|
||||
grid[inds] <- 2
|
||||
|
||||
alpha <- matrix(1e-5, ncol = cols, nrow = rows)
|
||||
alpha[inds] <- 1e-7
|
||||
|
||||
## image(grid, asp=1)
|
||||
|
||||
## Define grid configuration for POET model
|
||||
grid_setup <- list(
|
||||
pqc_in_file = "./barite_fgcs_2.pqi",
|
||||
pqc_db_file = "../barite/db_barite.dat", ## database file
|
||||
grid_def = grid, ## grid definition, IDs according to the Phreeqc input
|
||||
grid_size = c(dim_cols, dim_rows), ## grid size in meters
|
||||
constant_cells = c() ## IDs of cells with constant concentration
|
||||
)
|
||||
|
||||
bound_length <- cols / 10
|
||||
|
||||
bound_N <- list(
|
||||
"type" = rep("constant", bound_length),
|
||||
"sol_id" = rep(3, bound_length),
|
||||
"cell" = seq(1, bound_length)
|
||||
)
|
||||
|
||||
bound_W <- list(
|
||||
"type" = rep("constant", bound_length),
|
||||
"sol_id" = rep(3, bound_length),
|
||||
"cell" = seq(1, bound_length)
|
||||
)
|
||||
bound_E <- list(
|
||||
"type" = rep("constant", bound_length),
|
||||
"sol_id" = rep(4, bound_length),
|
||||
"cell" = seq(rows - bound_length + 1, rows)
|
||||
)
|
||||
|
||||
bound_S <- list(
|
||||
"type" = rep("constant", bound_length),
|
||||
"sol_id" = rep(4, bound_length),
|
||||
"cell" = seq(cols - bound_length + 1, cols)
|
||||
)
|
||||
|
||||
diffusion_setup <- list(
|
||||
boundaries = list(
|
||||
"W" = bound_W,
|
||||
"N" = bound_N,
|
||||
"E" = bound_E,
|
||||
"S" = bound_S
|
||||
),
|
||||
alpha_x = alpha,
|
||||
alpha_y = alpha
|
||||
)
|
||||
|
||||
dht_species <- c(
|
||||
"H" = 7,
|
||||
"O" = 7,
|
||||
"Ba" = 7,
|
||||
"Cl" = 7,
|
||||
"S" = 7,
|
||||
"Sr" = 7,
|
||||
"Barite" = 4,
|
||||
"Celestite" = 4
|
||||
)
|
||||
|
||||
pht_species <- c(
|
||||
"Ba" = 4,
|
||||
"Cl" = 3,
|
||||
"S" = 3,
|
||||
"Sr" = 3,
|
||||
"Barite" = 0,
|
||||
"Celestite" = 0
|
||||
)
|
||||
|
||||
chemistry_setup <- list(
|
||||
dht_species = dht_species,
|
||||
pht_species = pht_species
|
||||
)
|
||||
|
||||
## Define a setup list for simulation configuration
|
||||
setup <- list(
|
||||
Grid = grid_setup, ## Parameters related to the grid structure
|
||||
Diffusion = diffusion_setup, ## Parameters related to the diffusion process
|
||||
Chemistry = chemistry_setup
|
||||
)
|
||||
|
||||
|
||||
iterations <- 100
|
||||
dt <- 200
|
||||
checkpoint_interval <- 20
|
||||
control_interval <- 20
|
||||
mape_threshold <- rep(3.5e-3, 13)
|
||||
#out_save <- seq(50, iterations, by = 50)
|
||||
|
||||
|
||||
list(
|
||||
timesteps = rep(dt, iterations),
|
||||
store_result = FALSE,
|
||||
#out_save = out_save,
|
||||
checkpoint_interval = checkpoint_interval,
|
||||
control_interval = control_interval,
|
||||
mape_threshold = mape_threshold
|
||||
)
|
||||
@ -1,49 +0,0 @@
|
||||
SOLUTION 1
|
||||
units mol/kgw
|
||||
water 1
|
||||
temperature 25
|
||||
pH 7.008
|
||||
pe 10.798
|
||||
S 6.205e-04
|
||||
Sr 6.205e-04
|
||||
END
|
||||
|
||||
SOLUTION 2
|
||||
units mol/kgw
|
||||
water 1
|
||||
temperature 25
|
||||
pH 7.008
|
||||
pe 10.798
|
||||
S 6.205e-04
|
||||
Sr 6.205e-04
|
||||
KINETICS 2
|
||||
Barite
|
||||
-m 0.00
|
||||
-parms 50. # reactive surface area
|
||||
-tol 1e-9
|
||||
Celestite
|
||||
-m 1
|
||||
-parms 10.0 # reactive surface area
|
||||
-tol 1e-9
|
||||
END
|
||||
|
||||
SOLUTION 3
|
||||
units mol/kgw
|
||||
water 1
|
||||
temperature 25
|
||||
Ba 0.1
|
||||
Cl 0.2
|
||||
END
|
||||
|
||||
SOLUTION 4
|
||||
units mol/kgw
|
||||
water 1
|
||||
temperature 25
|
||||
Ba 0.2
|
||||
Cl 0.4
|
||||
END
|
||||
|
||||
|
||||
RUN_CELLS
|
||||
-cells 1 2 3 4
|
||||
END
|
||||
Binary file not shown.
43
bin/dol.pqi
43
bin/dol.pqi
@ -1,43 +0,0 @@
|
||||
SOLUTION 1
|
||||
units mol/kgw
|
||||
water 1
|
||||
temperature 25
|
||||
pH 7
|
||||
pe 4
|
||||
PURE 1
|
||||
Calcite 0.0 1
|
||||
END
|
||||
|
||||
RUN_CELLS
|
||||
-cells 1
|
||||
|
||||
COPY solution 1 2
|
||||
|
||||
PURE 2
|
||||
O2g -0.1675 10
|
||||
KINETICS 2
|
||||
Calcite
|
||||
-m 0.000207
|
||||
-parms 0.05
|
||||
-tol 1e-10
|
||||
Dolomite
|
||||
-m 0.0
|
||||
-parms 0.005
|
||||
-tol 1e-10
|
||||
END
|
||||
|
||||
SOLUTION 3
|
||||
units mol/kgw
|
||||
water 1
|
||||
temp 25
|
||||
Mg 0.001
|
||||
Cl 0.002
|
||||
END
|
||||
|
||||
SOLUTION 4
|
||||
units mol/kgw
|
||||
water 1
|
||||
temp 25
|
||||
Mg 0.002
|
||||
Cl 0.004
|
||||
END
|
||||
@ -1,135 +0,0 @@
|
||||
rows <- 400
|
||||
cols <- 400
|
||||
|
||||
grid_def <- matrix(2, nrow = rows, ncol = cols)
|
||||
|
||||
# Define grid configuration for POET model
|
||||
grid_setup <- list(
|
||||
pqc_in_file = "./dolo_fgcs.pqi",
|
||||
pqc_db_file = "./phreeqc_kin.dat", # Path to the database file for Phreeqc
|
||||
grid_def = grid_def, # Definition of the grid, containing IDs according to the Phreeqc input script
|
||||
grid_size = c(5, 5), # Size of the grid in meters
|
||||
constant_cells = c() # IDs of cells with constant concentration
|
||||
)
|
||||
|
||||
bound_def_we <- list(
|
||||
"type" = rep("constant", rows),
|
||||
"sol_id" = rep(1, rows),
|
||||
"cell" = seq(1, rows)
|
||||
)
|
||||
|
||||
bound_def_ns <- list(
|
||||
"type" = rep("constant", cols),
|
||||
"sol_id" = rep(1, cols),
|
||||
"cell" = seq(1, cols)
|
||||
)
|
||||
|
||||
diffusion_setup <- list(
|
||||
boundaries = list(
|
||||
"W" = bound_def_we,
|
||||
"E" = bound_def_we,
|
||||
"N" = bound_def_ns,
|
||||
"S" = bound_def_ns
|
||||
),
|
||||
inner_boundaries = list(
|
||||
"row" = floor(rows / 2),
|
||||
"col" = floor(cols / 2),
|
||||
"sol_id" = c(3)
|
||||
),
|
||||
alpha_x = 1e-6,
|
||||
alpha_y = 1e-6
|
||||
)
|
||||
|
||||
check_sign_cal_dol_dht <- function(old, new) {
|
||||
if ((old["Calcite"] == 0) != (new["Calcite"] == 0)) {
|
||||
return(TRUE)
|
||||
}
|
||||
if ((old["Dolomite"] == 0) != (new["Dolomite"] == 0)) {
|
||||
return(TRUE)
|
||||
}
|
||||
return(FALSE)
|
||||
}
|
||||
|
||||
check_sign_cal_dol_interp <- function(to_interp, data_set) {
|
||||
dht_species <- c(
|
||||
"H" = 3,
|
||||
"O" = 3,
|
||||
"C" = 6,
|
||||
"Ca" = 6,
|
||||
"Cl" = 3,
|
||||
"Mg" = 5,
|
||||
"Calcite" = 4,
|
||||
"Dolomite" = 4
|
||||
)
|
||||
data_set <- as.data.frame(do.call(rbind, data_set), check.names = FALSE, optional = TRUE)
|
||||
names(data_set) <- names(dht_species)
|
||||
cal <- (data_set$Calcite == 0) == (to_interp["Calcite"] == 0)
|
||||
dol <- (data_set$Dolomite == 0) == (to_interp["Dolomite"] == 0)
|
||||
|
||||
cal_dol_same_sig <- cal == dol
|
||||
return(rev(which(!cal_dol_same_sig)))
|
||||
}
|
||||
|
||||
check_neg_cal_dol <- function(result) {
|
||||
neg_sign <- (result["Calcite"] < 0) || (result["Dolomite"] < 0)
|
||||
return(neg_sign)
|
||||
}
|
||||
|
||||
# Optional when using Interpolation (example with less key species and custom
|
||||
# significant digits)
|
||||
|
||||
pht_species <- c(
|
||||
"C" = 3,
|
||||
"Ca" = 3,
|
||||
"Mg" = 3,
|
||||
"Cl" = 3,
|
||||
"Calcite" = 3,
|
||||
"Dolomite" = 3
|
||||
)
|
||||
|
||||
|
||||
dht_species <- c(
|
||||
"H" = 3,
|
||||
"O" = 3,
|
||||
"C" = 6,
|
||||
"Ca" = 6,
|
||||
"Cl" = 3,
|
||||
"Mg" = 5,
|
||||
"Calcite" = 4,
|
||||
"Dolomite" = 4)
|
||||
|
||||
chemistry_setup <- list(
|
||||
dht_species = dht_species,
|
||||
pht_species = pht_species,
|
||||
hooks = list(
|
||||
dht_fill = check_sign_cal_dol_dht,
|
||||
interp_pre = check_sign_cal_dol_interp,
|
||||
interp_post = check_neg_cal_dol
|
||||
)
|
||||
)
|
||||
|
||||
# Define a setup list for simulation configuration
|
||||
setup <- list(
|
||||
Grid = grid_setup, # Parameters related to the grid structure
|
||||
Diffusion = diffusion_setup, # Parameters related to the diffusion process
|
||||
Chemistry = chemistry_setup # Parameters related to the chemistry process
|
||||
)
|
||||
|
||||
iterations <- 5000
|
||||
dt <- 200
|
||||
checkpoint_interval <- 100
|
||||
control_interval <- 100
|
||||
mape_threshold <- rep(3.5e-3, 13)
|
||||
mape_threshold[5] <- 1 #Charge
|
||||
out_save <- seq(1000, iterations, by = 1000)
|
||||
out_save = c(seq(1, 10), seq(10, 100, by= 10), seq(200, iterations, by=100))
|
||||
|
||||
|
||||
list(
|
||||
timesteps = rep(dt, iterations),
|
||||
store_result = FALSE,
|
||||
out_save = out_save,
|
||||
checkpoint_interval = checkpoint_interval,
|
||||
control_interval = control_interval,
|
||||
mape_threshold = mape_threshold
|
||||
)
|
||||
Binary file not shown.
1307
bin/phreeqc_kin.dat
1307
bin/phreeqc_kin.dat
File diff suppressed because it is too large
Load Diff
@ -1,18 +0,0 @@
|
||||
#!/bin/bash
|
||||
#SBATCH --job-name=dolo_5000_no_charge
|
||||
#SBATCH --output=dolo_5000_no_charge_%j.out
|
||||
#SBATCH --error=dolo_5000_no_charge_%j.err
|
||||
#SBATCH --partition=long
|
||||
#SBATCH --nodes=6
|
||||
#SBATCH --ntasks-per-node=24
|
||||
#SBATCH --ntasks=144
|
||||
#SBATCH --exclusive
|
||||
#SBATCH --time=12:00:00
|
||||
|
||||
|
||||
source /etc/profile.d/modules.sh
|
||||
module purge
|
||||
module load cmake gcc openmpi
|
||||
|
||||
mpirun -n 144 ./poet --interp dolo_fgcs_3.R dolo_fgcs_3.qs2 dolo_5000_no_charge
|
||||
##mpirun -n 96 ./poet --interp barite_fgcs_2.R barite_fgcs_2.qs2 bar_warmup
|
||||
Loading…
x
Reference in New Issue
Block a user